| Metadata |
| datasetIdentifier | PASS01544 |
| datasetType | SRM |
| submitter | Leena Liljedahl <leena.liljedahl@immun.lth.se> |
| submitter_organization | Department of Immunotechnology, Lund University |
| lab_head_full_name | Carl Borrebaeck |
| lab_head_email | carl.borrebaeck@immun.lth.se |
| lab_head_organization | CREATE Health, Lund University |
| lab_head_country | Sweden |
| datasetTag | EOC_subtypes |
| datasetTitle | Epithelial ovarian cancer subgroup characterization in plasma using SRM-MS, based on EOC cyst fluid and tumour tissue findings, complemented with literature search |
| publicReleaseDate | 2021-11-10 00:00:00 |
| finalizedDate | |
| summary | Plasma with depletion of 14 most abundant plasma proteins (Agilent), nearly 400 synthetic peptides from JPT Berlin, tested in plasma pools, targeted final assay with 166 peptides, 159 protein, 18 control peptides, 11 depleted proteins. Protein selection based on previous cyst fluid and EOC tumour tissue MS analysis and literature in association to EOC. Samples collected at Sahlgrenska Akademiska sjukhus, Gothenburg, Sweden 2012-2015, 74 samples in total from benign ovarian cysts (cystadenofibromas n=14, cystadenomas, n=2), epithelial ovarian cancer (EOC; borderline type tumours n=13, endometrioid stage I-II n=7, mucinous stage I-II n=9, serous lowgrade stage I-II n=4, serous highgrade stage I-II n=8 and serous highgrade stage III n=17. Skyline and Anubis processing FDR of 0.01, NormalyzerDE with Loess global normalisation, Qlucore PCA, SIMCA OPLS-DA, Bionamic ROC AUC calculation using SVM and signatures selection based on variables of importance in OPLS-DA analysis and/or p-value, and LASSO. Comparison on different levels; benign vs all malignant, benign vs. grade, stage, type, subgroup. |
| contributors | Leena Liljedahl
Simon Hauri
Ola Kilsgård
Johan Malmström
Sofia Waldemarsson
Karin Sundfeldt |
| publication | unpublished Leena Liljedahl, Simon Hauri, Ola Kilsgård, Johan Malmström, Sofia Waldemarson, Karin Sundfeldt TITLE JOURNAL |
| growth | Plasma with Agilent depletion of 14 most abundant plasma proteins. Followed by trypsin digestion and c18 cleanup. |
| treatment | Blood samples taken at time of surgery, after anaesthesia was given. |
| extraction | |
| separation | |
| digestion | Trypsin based digestion |
| acquisition | |
| informatics | Skyline and Anubis processing, FDR of 0.01
Loess Global/cyclic through NormalyzerDE evaluation.
Principal component analysis, ANOVA and t-tests.
OPLS-DA / supervised analysis in SIMCA |
| instruments | Thermo Scientific TSQ Quantiva |
| species | Human |
| massModifications | none |
